Changing directions in Pol III transcription

RNA polymerase III transcription control elements: themes and variations

Eukaryotic genomes are punctuated by a multitude of tiny genetic elements, that share the property of being recognized and transcribed by the RNA polymerase (Pol) III machinery to produce a variety of small, abundant non-protein-coding (nc) RNAs (tRNAs, 5S rRNA, U6 snRNA and many others). The highly selective, efficient and localized action of Pol III at its minute genomic targets is made possible by a handful of cis-acting regulatory elements, located within the transcribed region (where they are bound by the multisubunit assembly factor TFIIIC) and/or upstream of the transcription start site. Most of them participate directly or indirectly in the ultimate recruitment of TFIIIB, a key multiprotein initiation factor able to direct, once assembled, multiple transcription cycles by Pol III. But the peculiar efficiency and selectivity of Pol III transcription also depends on its ability to recognize very simple and precisely positioned termination signals. Studies in the last few years have significantly expanded the set of known Pol III-associated loci in genomes and, concomitantly, have revealed unexpected features of Pol III cis-regulatory elements in terms of variety, function, genomic location and potential contribution to transcriptome complexity. Here we review, in a historical perspective, well established and newly acquired knowledge about Pol III transcription control elements, with the aim of providing a useful reference for future studies of the Pol III system, which we anticipate will be numerous and intriguing for years to come.

BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript

Rodent BC1 RNA represents the first example of a neural cell-specific RNA polymerase III (Pol III) transcription product. By developing a rat brain in vitro system capable of supporting Pol III-directed transcription, we showed that the rat BC1 RNA intragenic promoter elements, comprising an A box element and a variant B box element, as well as its upstream region, containing octamer-binding consensus sequences and functional TATA and proximal sequence element sites, are necessary for transcription. The BC1 B box, lacking the invariant A residue found in the consensus B boxes of tRNAs, represents a functionally related and possibly distinct promoter element. The transcriptional activity of the BC1 B box element is greatly increased, in both a BC1 RNA and a chimeric tRNA(Leu) gene construct, when the BC1 5' flanking region is present and is appropriately spaced. Moreover, a tRNA consensus B-box sequence can efficiently replace the BC1 B box only if the BC1 upstream region is removed. These interactions, identified only in a homologous in vitro system, between upstream Pol II and intragenic Pol III promoters suggest a mechanism by which the tissue-specific BC1 RNA gene and possibly other Pol III-transcribed genes can be regulated.

In vitro and in vivo analysis of the c-myc RNA polymerase III promoter

The c-myc promoter has the unusual property of displaying both RNA polymerase II (Pol II) and RNA polymerase III (Pol III) activities. Both Pol II and Pol III utilize the same transcription initiation site. We have now examined the effects of mutations in crucial regions of the c-myc promoter to assess their effects on both transcriptional activities. In doing this we show that both Pol II and Pol III activities require sequences that are located within the stronger of the two principal c-myc promoter regions (P2). Further, we show that the Pol III activity using this initiation site does not require an A box or distal upstream sequences. Like the Pol II activity, it does require an intact TATA sequence and alterations at this site result in the simultaneous loss of both Pol II and Pol III activities. The superimposition of two apparently inseparable promoter activities makes it possible to consider common features, possible common protein elements in each holoenzyme complex, as well as a potential role for each enzyme in the regulated expression of the c-myc gene.

Primary structure and functional aspects of the gene coding for the second-largest subunit of RNA polymerase III of Drosophila

We have cloned and sequenced the gene coding for the second-largest subunit of RNA polymerase III of Drosophila melanogaster (DmRP135). The gene, interrupted by two introns of 62 and 59 bp, respectively, codes for an mRNA of 3.6 kb. As for other housekeeping genes transcription initiates at several sites (between positions -98 and -76) none of which is preceded by a clear TATA sequence. The deduced polypeptide consists of 1129 amino acids with an aggregate molecular weight of 128 kDa. The protein sequence features the same regions of similarity as observed for the corresponding subunits of RNA polymerase II of Drosophila and yeast and the Escherichia coli beta subunit. As in the second-largest subunit of RNA polymerase II there is a zinc-binding motif which is absent in the beta subunit of E. coli. Antibodies directed against a fusion protein expressing 164 amino acids of the DmRP135 polypeptide cross-react with the second-largest subunit of RNA polymerase III of yeast and generate a distinct banding pattern on Drosophila polytene chromosomes distinguishable from that obtained with anti-RNA polymerase II antibodies.

Transcription of a human U6 small nuclear RNA gene in vivo withstands deletion of intragenic sequences but not of an upstream TATATA box

Most eukaryotic genes transcribed by RNA polymerase III contain internal control regions. U6 small nuclear RNA genes are transcribed by RNA polymerase III but are unusual in that, at least in vitro, their expression does not require intragenic sequences. Here we show that this is true as well in vivo. A human U6 gene devoid of all but the first 6 and last 10 base-pairs was expressed efficiently after transfection into human 293 cells. We also report data extending the previous identification of 5' flanking sequences important for human U6 gene transcription. Deletion-substitution of a 10 base-pair upstream sequence encompassing the TATATA element (-29 to -24) abolished U6 transcription. A double point mutation in the middle of this element (TATATA-TAGCTA) reduced U6 transcription but not to the extent brought about by TATATA deletion-substitution. These results establish that, in vivo, transcription of human U6 small nuclear RNA is independent of intragenic sequences between nucleotides 6 and 98, and requires the upstream TATATA box.

Accurate, TATA box-dependent polymerase III transcription from promoters of the c-myc gene in injected Xenopus oocytes

We have investigated the factors that permit a gene normally transcribed by RNA polymerase II to be transcribed by RNA polymerase III. It was shown previously that the human c-myc gene could be transcribed in vitro and in Xenopus oocytes by both alpha-amanitin-sensitive and alpha-amanitin-resistant polymerases, probably corresponding to polymerase II and polymerase III. We confirmed this observation in microinjected oocytes and showed that the alpha-amanitin-resistant transcription of c-myc was competed by known polymerase III genes. Polymerase III transcription of c-myc was very inefficient compared to other polymerase III genes, however, and was observed only when large amounts of template DNA were injected. At lower DNA concentrations the gene was transcribed, exclusively by polymerase II. In contrast, the adenovirus major late promoter was not transcribed by polymerase III. The 5' ends of polymerase III RNAs were almost indistinguishable from those of polymerase II RNAs initiating at the P1 and P2 promoters of the human and mouse c-myc genes. Furthermore, point mutations in the TATA box of the human P2 promoter greatly reduced polymerase III activity. At this promoter, therefore, polymerase II and polymerase III recognize a common element, the TATA box, which probably plays an important role in specifying the start site of transcription for both polymerases. We suggest that the highly accurate though inefficient mimicry of polymerase II by polymerase III at the c-myc promoters reflects the common evolutionary origin of these two enzymes.

Presence of multiple species of polypeptides immunologically related to transcription factor TFIIIA in adult Xenopus tissues

Transcription of 5S RNA gene in Xenopus oocytes requires a 38 kDa transcription factor TFIIIA, which interacts with the 50 bp internal control region of the gene. We looked for TFIIIA-like polypeptides in the extracts of adult Xenopus tissues on the basis of their antigenic cross-reactivity to anti-TFIIIA antibody. Several species of polypeptides ranging from 30 to 50 kDa were found in kidney, stomach, liver and testis. Although these polypeptides reacted specifically to anti-TFIIIA antibody, proteolytic peptide mapping of three representative ones did not reveal any mutual similarities. They also seemed to be distinct from TFIIIA. Possible functions of these proteins are discussed.

The C-terminal domain of transcription factor IIIA interacts differently with different 5S RNA genes

DNase I footprints and affinity measurements showed that the C-terminal arm of Xenopus transcription factor IIIA interacts differently with different Xenopus 5S DNAs, forming three distinct types of transcription factor IIIA-5S DNA complexes: a somatic type, a major-oocyte (and pseudogene) type, and a trace-oocyte type. Site-directed mutagenesis on the major-oocyte 5S gene revealed that somatic-type changes at positions 53, 55, and 56 changed the structure of the transcription factor IIIA-5S DNA complex from major-oocyte to somatic, and a single trace-oocyte change at position 56 caused the change from major-oocyte to trace-oocyte complex. We further show that the somatic-type changes are accompanied by a marked enhancement in the rate of 5S RNA transcription, and we discuss the possible biological relevance of these findings.

The C-terminal domain of transcription factor IIIA interacts differently with different 5S RNA genes

DNase I footprints and affinity measurements showed that the C-terminal arm of Xenopus transcription factor IIIA interacts differently with different Xenopus 5S DNAs, forming three distinct types of transcription factor IIIA-5S DNA complexes: a somatic type, a major-oocyte (and pseudogene) type, and a trace-oocyte type. Site-directed mutagenesis on the major-oocyte 5S gene revealed that somatic-type changes at positions 53, 55, and 56 changed the structure of the transcription factor IIIA-5S DNA complex from major-oocyte to somatic, and a single trace-oocyte change at position 56 caused the change from major-oocyte to trace-oocyte complex. We further show that the somatic-type changes are accompanied by a marked enhancement in the rate of 5S RNA transcription, and we discuss the possible biological relevance of these findings.

An efficiently transcribed human tRNA(Val) gene variant produces a stable pre-tRNA: repair of the processing defect by in vitro mutations

A tRNA(CACVal) gene variant, pHtV4, was cloned from human placenta genomic DNA. This gene differs from a closely related, functional tRNA(CACVal) gene by four base exchanges: T residues in place of C25, C62, and C66 create G:U pairs, and an A instead of G65 creates an A:C mismatch in the corresponding RNA transcript. The tRNA(Val) gene variant in pHtV4 is efficiently transcribed in HeLa cell nuclear extracts; however, the resulting pre-tRNA is processing-deficient, i.e., neither its 5'- nor its 3'-flanking sequences are removed to generate mature tRNA. Reversion of all four point mutations in pHtV4 by oligonucleotide-directed mutagenesis yielded a functional tRNA(CACVal) gene within the flanks of pHtV4, the pre-tRNA of which was processed to mature tRNA. Construction of a chimeric tRNA(Val) gene and site-directed mutagenesis of the tRNA(Val) gene in pHtV4, respectively, followed by transcription and processing studies showed that each of the four mutations contributes to the processing defect of the pHtV4-derived pre-tRNA. Moreover, this revealed that G:U pairs, which are common in all tRNAs, can impair pre-tRNA processing and therefore do not occur in certain positions in eukaryotic tRNAs.

Octamer-binding proteins from B or HeLa cells stimulate transcription of the immunoglobulin heavy-chain promoter in vitro

The B-cell-type specificity of the immunoglobulin (Ig) heavy-chain and light-chain promoters is mediated by an octanucleotide (OCTA) element, ATGCAAAT, that is also a functional component of other RNA polymerase II promoters, such as snRNA and histone H2B promoters. Two nuclear proteins that bind specifically and with high affinity to the OCTA element have been identified. NF-A1 is present in a variety of cell types, whereas the presence of NF-A2 is essentially confined to B cells, leading to the hypothesis that NF-A2 activates cell-type-specific transcription of the Ig promoter and NF-A1 mediates the other responses of the OCTA element. Extracts of the B-cell line, BJA-B, contain high levels of NF-A2 and specifically transcribe Ig promoters. In contrast, extracts from HeLa cells transcribed the Ig promoter poorly. Surprisingly, addition of either affinity-enriched NF-A2 or NF-A1 to either a HeLa extract or a partially purified reaction system specifically stimulates the Ig promoter. This suggests that the constitutive OCTA-binding factor NF-A1 can activate transcription of the Ig promoter and that B-cell-specific transcription of this promoter, at least in vitro, is partially due to a quantitative difference in the amount of OCTA-binding protein. Because NF-A1 can stimulate Ig transcription, the inability of this factor to activate in vivo the Ig promoter to the same degree as the snRNA promoters probably reflects a difference in the context of the OCTA element in these two types of promoters.